Fixes according to Marc's review

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2881 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 84870193cb05cabd8c756a3bbc49083e4d739525

4 files changed, 215 insertions, 56 deletions

diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index 6a602dbb..9677f5c5 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -3,15 +3,15 @@ project(Bottleneck_distance_examples)
 
 if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
-  add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
+  add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
+  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
   add_test(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>)
+  add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck
+      COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
 
-  add_test(NAME Bottleneck_read_file_example
-      COMMAND $<TARGET_FILE:bottleneck_read_file_example>
-      "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers")
-
-  install(TARGETS bottleneck_read_file_example DESTINATION bin)
   install(TARGETS bottleneck_basic_example DESTINATION bin)
+  install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
   
 endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/example/README b/src/Bottleneck_distance/example/README
new file mode 100644
index 00000000..0e314608
--- /dev/null
+++ b/src/Bottleneck_distance/example/README
@@ -0,0 +1,19 @@
+# Bottleneck_distance #

+

+## `alpha_rips_persistence_bottleneck_distance` ##

+This program computes the persistent homology with coefficient field Z/pZ of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:

+

+`p dim b d`

+

+where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.

+

+Usage:

+`alpha_rips_persistence_bottleneck_distance [options] <OFF input file>`

+

+Allowed options:

+

+* `-h [ --help ]` Produce help message

+* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction.`

+* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute.`

+* `-p [ --field-charac ]` (default = 11)     Characteristic p of the coefficient field Z/pZ for computing homology.

+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.

diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
new file mode 100644
index 00000000..fd164b22
--- /dev/null
+++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
@@ -0,0 +1,190 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2017  INRIA
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/Alpha_complex.h>
+#include <gudhi/Rips_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/Bottleneck.h>
+
+#include <CGAL/Epick_d.h>
+
+#include <boost/program_options.hpp>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+#include <utility>  // for pair
+#include <algorithm>  // for transform
+
+
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+using Point_d = Kernel::Point_d;
+using Points_off_reader = Gudhi::Points_off_reader<Point_d>;
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+static inline std::pair<double, double> compute_root_square(std::pair<double, double> input) {
+  return std::make_pair(std::sqrt(input.first), std::sqrt(input.second));
+}
+
+int main(int argc, char * argv[]) {
+  std::string off_file_points;
+  Filtration_value threshold;
+  int dim_max;
+  int p;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, off_file_points, threshold, dim_max, p, min_persistence);
+
+  Points_off_reader off_reader(off_file_points);
+
+  // --------------------------------------------
+  // Rips persistence
+  // --------------------------------------------
+  Rips_complex rips_complex(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
+
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree rips_stree;
+
+  rips_complex.create_complex(rips_stree, dim_max);
+  std::cout << "The Rips complex contains " << rips_stree.num_simplices() << " simplices and has dimension "
+            << rips_stree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  rips_stree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology rips_pcoh(rips_stree);
+  // initializes the coefficient field for homology
+  rips_pcoh.init_coefficients(p);
+  rips_pcoh.compute_persistent_cohomology(min_persistence);
+
+  // rips_pcoh.output_diagram();
+
+  // --------------------------------------------
+  // Alpha persistence
+  // --------------------------------------------
+  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex(off_reader.get_point_cloud());
+
+  Simplex_tree alpha_stree;
+  alpha_complex.create_complex(alpha_stree, threshold * threshold);
+  std::cout << "The Alpha complex contains " << alpha_stree.num_simplices() << " simplices and has dimension "
+            << alpha_stree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  alpha_stree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology alpha_pcoh(alpha_stree);
+  // initializes the coefficient field for homology
+  alpha_pcoh.init_coefficients(p);
+  alpha_pcoh.compute_persistent_cohomology(min_persistence * min_persistence);
+
+  // alpha_pcoh.output_diagram();
+
+  // --------------------------------------------
+  // Bottleneck distance between both persistence
+  // --------------------------------------------
+  double max_b_distance {};
+  for (int dim = 0; dim < dim_max; dim ++) {
+    std::vector< std::pair< Filtration_value , Filtration_value > > rips_intervals;
+    std::vector< std::pair< Filtration_value , Filtration_value > > alpha_intervals;
+    rips_intervals = rips_pcoh.intervals_in_dimension(dim);
+    alpha_intervals = alpha_pcoh.intervals_in_dimension(dim);
+    std::transform(alpha_intervals.begin(), alpha_intervals.end(), alpha_intervals.begin(), compute_root_square);
+
+    double bottleneck_distance = Gudhi::persistence_diagram::bottleneck_distance(rips_intervals, alpha_intervals);
+    std::cout << "In dimension " << dim << ", bottleneck distance = " << bottleneck_distance << std::endl;
+    if (bottleneck_distance > max_b_distance)
+      max_b_distance = bottleneck_distance;
+  }
+  std::cout << "================================================================================" << std::endl;
+  std::cout << "Bottleneck distance is " << max_b_distance << std::endl;
+
+  return 0;
+}
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence) {
+  namespace po = boost::program_options;
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&off_file_points),
+       "Name of an OFF file containing a point set.\n");
+
+  po::options_description visible("Allowed options", 100);
+  visible.add_options()
+      ("help,h", "produce help message")
+      ("max-edge-length,r",
+       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+       "Maximal length of an edge for the Rips complex construction.")
+      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
+       "Maximal dimension of the Rips complex we want to compute.")
+      ("field-charac,p", po::value<int>(&p)->default_value(11),
+       "Characteristic p of the coefficient field Z/pZ for computing homology.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+
+  po::positional_options_description pos;
+  pos.add("input-file", 1);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
+
+  po::variables_map vm;
+  po::store(po::command_line_parser(argc, argv).
+            options(all).positional(pos).run(), vm);
+  po::notify(vm);
+
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of a Rips complex defined on a set of input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}
diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
deleted file mode 100644
index 24d73c57..00000000
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ /dev/null
@@ -1,50 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Authors:       Francois Godi, small modifications by Pawel Dlotko
- *
- *    Copyright (C) 2015  INRIA
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <gudhi/Bottleneck.h>
-#include <gudhi/reader_utils.h>
-#include <iostream>
-#include <vector>
-#include <utility>  // for pair
-#include <string>
-#include <limits>  // for numeric_limits
-
-int main(int argc, char** argv) {
-  if (argc < 3) {
-    std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file" <<
-        " should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
-        " distance (set by default to the smallest positive double value). If you set the error bound to 0, be" <<
-        " aware this version is exact but expensive. The program will now terminate \n";
-    return -1;
-  }
-  std::vector<std::pair<double, double>> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]);
-  std::vector<std::pair<double, double>> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]);
-
-  double tolerance = std::numeric_limits<double>::min();
-  if (argc == 4) {
-    tolerance = atof(argv[3]);
-  }
-  double b = Gudhi::persistence_diagram::bottleneck_distance(diag1, diag2, tolerance);
-  std::cout << "The distance between the diagrams is : " << b << ". The tolerance is : " << tolerance << std::endl;
-
-  return 0;
-}